5BR1

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS S4 (Avi_5305, TARGET EFI-511224) WITH BOUND ALPHA-D-GALACTOSAMINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IOY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298Protein (53.5 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-galactosamine); Reservoir (42.1 %(w/v) PEG 4000); Cryoprotection (Reservoir, Pause in air during transfer to liquid N2)
Crystal Properties
Matthews coefficientSolvent content
1.8734.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.781α = 90
b = 63.701β = 90
c = 119.575γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2015-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54056

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8516.6870.1270.1410.0596.84.92155321.92
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8864.80.6080.7310.3970.5262.8782

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2IOY1.8516.4991.3720961103284.660.18770.18270.282834.6342
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.543
f_angle_d1.397
f_chiral_restr0.061
f_bond_d0.013
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2381
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms12

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-3000data reduction